AMBER: Any correct way to image a molecule ?

From: Teletchéa Stéphane <>
Date: Thu, 13 Nov 2003 22:37:40 +0100

I'm use to image my DNA strands with ptraj. The input file is generally
trajin dn300K1_c.gz
trajin dn300K2_c.gz
trajout dn300K.crd nobox
strip :CIP
strip :WAT
center origin
image center familiar

And it is able to bring back my two strands in the same box, so i can
visualise it correctly.

I'm now trying to find a way to do the same for the counter-ions and may
be some water molecules. But there, i'm encountering an imaging problem
: i've tried to be more precise in the centering, used masks, tried to
not remove conter-ions or even water (that makes a big trajectory).

I'm never getting one solely box, but at least what seems to be 4 or 8.

I've tried to change the size of the prmtop input file (the size of the
box is somehow diminished during the run : coming from 62/52/51 to
60/50/50), but now i'm not able to image the counter-ions.

I'm using ptraj from AMBER6, with suposedly all latest patches.

Any hint ?

Thank you in advance,

Stéphane Teletchéa
22:37:23 up 8:46, 9 users, load average: 0.00, 0.03, 0.14 
Linux 2.4.22-10stef.2mdkcustom #1 dim oct 26 23:59:10 CET 2003

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Received on Thu Nov 13 2003 - 21:53:00 PST
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